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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8067 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-05-17 17:05:05 +00:00
parent 8fb0508d38
commit 09740d261b
1 changed files with 57 additions and 55 deletions
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112
src/read_data.cpp
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@ -374,6 +374,23 @@ void ReadData::header(int flag)
if (strstr(line,"atoms")) sscanf(line,BIGINT_FORMAT,&atom->natoms); if (strstr(line,"atoms")) sscanf(line,BIGINT_FORMAT,&atom->natoms);
// check for these first
// otherwise "triangles" will be matched as "angles"
else if (strstr(line,"ellipsoids")) {
if (!avec_ellipsoid && me == 0)
error->one(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
} else if (strstr(line,"lines")) {
if (!avec_line && me == 0)
error->one(FLERR,"No lines allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nlines);
} else if (strstr(line,"triangles")) {
if (!avec_tri && me == 0)
error->one(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
}
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds); else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles); else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT, else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT,
@ -392,20 +409,6 @@ void ReadData::header(int flag)
else if (strstr(line,"extra bond per atom")) else if (strstr(line,"extra bond per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom); sscanf(line,"%d",&atom->extra_bond_per_atom);
else if (strstr(line,"ellipsoids")) {
if (!avec_ellipsoid)
error->all(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
} else if (strstr(line,"lines")) {
if (!avec_line)
error->all(FLERR,"No lines allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nlines);
} else if (strstr(line,"triangles")) {
if (!avec_tri)
error->all(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
}
else if (strstr(line,"xlo xhi")) else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]); sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
else if (strstr(line,"ylo yhi")) else if (strstr(line,"ylo yhi"))
@ -425,8 +428,7 @@ void ReadData::header(int flag)
atom->nangles < 0 || atom->nangles > MAXBIGINT || atom->nangles < 0 || atom->nangles > MAXBIGINT ||
atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT || atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT ||
atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) { atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) {
if (flag == 0) error->one(FLERR,"System in data file is too big"); if (me == 0) error->one(FLERR,"System in data file is too big");
else error->all(FLERR,"System in data file is too big");
} }
// check that exiting string is a valid section keyword // check that exiting string is a valid section keyword
@ -434,34 +436,34 @@ void ReadData::header(int flag)
parse_keyword(1,flag); parse_keyword(1,flag);
for (n = 0; n < NSECTIONS; n++) for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break; if (strcmp(keyword,section_keywords[n]) == 0) break;
if (n == NSECTIONS) { if (n == NSECTIONS && me == 0) {
char str[128]; char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword); sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(FLERR,str); error->one(FLERR,str);
} }
// error check on consistency of header values // error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) && if ((atom->nbonds || atom->nbondtypes) &&
atom->avec->bonds_allow == 0) atom->avec->bonds_allow == 0 && me == 0)
error->one(FLERR,"No bonds allowed with this atom style"); error->one(FLERR,"No bonds allowed with this atom style");
if ((atom->nangles || atom->nangletypes) && if ((atom->nangles || atom->nangletypes) &&
atom->avec->angles_allow == 0) atom->avec->angles_allow == 0 && me == 0)
error->one(FLERR,"No angles allowed with this atom style"); error->one(FLERR,"No angles allowed with this atom style");
if ((atom->ndihedrals || atom->ndihedraltypes) && if ((atom->ndihedrals || atom->ndihedraltypes) &&
atom->avec->dihedrals_allow == 0) atom->avec->dihedrals_allow == 0 && me == 0)
error->one(FLERR,"No dihedrals allowed with this atom style"); error->one(FLERR,"No dihedrals allowed with this atom style");
if ((atom->nimpropers || atom->nimpropertypes) && if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0) atom->avec->impropers_allow == 0 && me == 0)
error->one(FLERR,"No impropers allowed with this atom style"); error->one(FLERR,"No impropers allowed with this atom style");
if (atom->nbonds > 0 && atom->nbondtypes <= 0) if (atom->nbonds > 0 && atom->nbondtypes <= 0 && me == 0)
error->one(FLERR,"Bonds defined but no bond types"); error->one(FLERR,"Bonds defined but no bond types");
if (atom->nangles > 0 && atom->nangletypes <= 0) if (atom->nangles > 0 && atom->nangletypes <= 0 && me == 0)
error->one(FLERR,"Angles defined but no angle types"); error->one(FLERR,"Angles defined but no angle types");
if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0) if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0 && me == 0)
error->one(FLERR,"Dihedrals defined but no dihedral types"); error->one(FLERR,"Dihedrals defined but no dihedral types");
if (atom->nimpropers > 0 && atom->nimpropertypes <= 0) if (atom->nimpropers > 0 && atom->nimpropertypes <= 0 && me == 0)
error->one(FLERR,"Impropers defined but no improper types"); error->one(FLERR,"Impropers defined but no improper types");
} }
@ -1037,7 +1039,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
char *eof; char *eof;
if (atom->natoms > MAXSMALLINT) if (atom->natoms > MAXSMALLINT)
error->all(FLERR,"Molecular data file has too many atoms"); error->one(FLERR,"Molecular data file has too many atoms");
// customize for new sections // customize for new sections
@ -1064,100 +1066,100 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else if (strcmp(keyword,"Ellipsoids") == 0) { else if (strcmp(keyword,"Ellipsoids") == 0) {
if (!avec_ellipsoid) if (!avec_ellipsoid)
error->all(FLERR,"Invalid data file section: Ellipsoids"); error->one(FLERR,"Invalid data file section: Ellipsoids");
ellipsoid_flag = 1; ellipsoid_flag = 1;
skip_lines(nellipsoids); skip_lines(nellipsoids);
} else if (strcmp(keyword,"Lines") == 0) { } else if (strcmp(keyword,"Lines") == 0) {
if (!avec_line) error->all(FLERR,"Invalid data file section: Lines"); if (!avec_line) error->one(FLERR,"Invalid data file section: Lines");
line_flag = 1; line_flag = 1;
skip_lines(nlines); skip_lines(nlines);
} else if (strcmp(keyword,"Triangles") == 0) { } else if (strcmp(keyword,"Triangles") == 0) {
if (!avec_tri) error->all(FLERR,"Invalid data file section: Triangles"); if (!avec_tri) error->one(FLERR,"Invalid data file section: Triangles");
tri_flag = 1; tri_flag = 1;
skip_lines(ntris); skip_lines(ntris);
} else if (strcmp(keyword,"Pair Coeffs") == 0) { } else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL) if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before Pair Coeffs"); error->one(FLERR,"Must define pair_style before Pair Coeffs");
skip_lines(atom->ntypes); skip_lines(atom->ntypes);
} else if (strcmp(keyword,"Bond Coeffs") == 0) { } else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0) if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Invalid data file section: Bond Coeffs"); error->one(FLERR,"Invalid data file section: Bond Coeffs");
if (force->bond == NULL) if (force->bond == NULL)
error->all(FLERR,"Must define bond_style before Bond Coeffs"); error->one(FLERR,"Must define bond_style before Bond Coeffs");
skip_lines(atom->nbondtypes); skip_lines(atom->nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) { } else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0) if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: Angle Coeffs"); error->one(FLERR,"Invalid data file section: Angle Coeffs");
if (force->angle == NULL) if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before Angle Coeffs"); error->one(FLERR,"Must define angle_style before Angle Coeffs");
skip_lines(atom->nangletypes); skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) { } else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: Dihedral Coeffs"); error->one(FLERR,"Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs"); error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
} else if (strcmp(keyword,"Improper Coeffs") == 0) { } else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0) if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: Improper Coeffs"); error->one(FLERR,"Invalid data file section: Improper Coeffs");
if (force->improper == NULL) if (force->improper == NULL)
error->all(FLERR,"Must define improper_style before Improper Coeffs"); error->one(FLERR,"Must define improper_style before Improper Coeffs");
skip_lines(atom->nimpropertypes); skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) { } else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0) if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: BondBond Coeffs"); error->one(FLERR,"Invalid data file section: BondBond Coeffs");
if (force->angle == NULL) if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before BondBond Coeffs"); error->one(FLERR,"Must define angle_style before BondBond Coeffs");
skip_lines(atom->nangletypes); skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) { } else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0) if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: BondAngle Coeffs"); error->one(FLERR,"Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL) if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before BondAngle Coeffs"); error->one(FLERR,"Must define angle_style before BondAngle Coeffs");
skip_lines(atom->nangletypes); skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) { } else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs"); error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR, error->one(FLERR,
"Must define dihedral_style before " "Must define dihedral_style before "
"MiddleBondTorsion Coeffs"); "MiddleBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) { } else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs"); error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR, error->one(FLERR,
"Must define dihedral_style before EndBondTorsion Coeffs"); "Must define dihedral_style before EndBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) { } else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs"); error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR, error->one(FLERR,
"Must define dihedral_style before AngleTorsion Coeffs"); "Must define dihedral_style before AngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) { } else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs"); error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR, error->one(FLERR,
"Must define dihedral_style before " "Must define dihedral_style before "
"AngleAngleTorsion Coeffs"); "AngleAngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) { } else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: BondBond13 Coeffs"); error->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL) if (force->dihedral == NULL)
error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs"); error->one(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
skip_lines(atom->ndihedraltypes); skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) { } else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0) if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: AngleAngle Coeffs"); error->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL) if (force->improper == NULL)
error->all(FLERR,"Must define improper_style before AngleAngle Coeffs"); error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
skip_lines(atom->nimpropertypes); skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"Bonds") == 0) { } else if (strcmp(keyword,"Bonds") == 0) {